Contacts of the helix formed by residues 448 - 460 (chain B) in PDB entry 2HD1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 448 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421B LEU* 4.2 3.8 - - - -
446B LYS 5.2 2.7 - - - +
447B VAL* 1.3 83.0 - - - +
449B LYS* 1.3 66.3 + - - +
450B ALA* 3.0 9.7 + - - +
451B THR* 3.0 33.8 + - + +
452B ALA* 3.0 22.0 + - - +
494B LYS* 5.9 0.2 - - - +
497B ASP* 4.8 12.9 + - + +
501B LYS* 4.8 18.2 - - - +
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Residues in contact with LYS 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B GLU* 2.6 38.8 + - - +
417B VAL* 3.9 29.8 - - + -
418B ASP* 3.0 39.8 + - - +
421B LEU* 4.0 13.9 - - + +
448B THR* 1.3 71.9 - - - +
450B ALA* 1.3 61.1 + - - +
452B ALA* 3.7 1.2 + - - +
453B GLN* 3.2 30.1 + - - +
490B TYR* 4.0 9.6 - - + -
493B LEU* 5.9 3.4 - - + -
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Residues in contact with ALA 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B THR* 3.0 7.7 + - - +
449B LYS* 1.3 75.8 - - - +
451B THR* 1.3 66.7 + - - +
452B ALA 3.1 1.3 + - - -
453B GLN* 3.3 1.0 + - - +
454B ILE* 3.0 31.7 + - - +
490B TYR* 3.9 34.2 - - + +
493B LEU* 4.7 6.0 - - + +
494B LYS* 4.1 17.5 - - + +
497B ASP* 4.2 13.2 - - - +
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Residues in contact with THR 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446B LYS 4.1 7.1 + - - +
447B VAL* 3.9 8.0 - - - +
448B THR* 3.0 39.1 + - + +
450B ALA* 1.3 78.3 - - - +
452B ALA* 1.3 61.6 + - - +
454B ILE* 4.1 9.5 + - - +
455B GLY* 4.2 7.6 + - - -
494B LYS* 4.5 26.5 - - + -
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Residues in contact with ALA 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B IBM 3.3 24.1 + - + -
417B VAL* 5.2 1.1 - - + -
420B LEU* 6.3 0.2 - - + -
421B LEU* 4.2 14.8 - - + -
424B TYR* 6.3 0.4 - - + -
441B PHE 5.8 1.3 - - - +
447B VAL* 3.9 16.8 - - + -
448B THR 3.0 16.5 + - - +
449B LYS* 3.8 5.2 - - - +
451B THR* 1.3 81.0 + - - +
453B GLN* 1.3 71.1 + - + +
455B GLY* 5.0 0.2 - - - -
456B PHE* 3.6 9.7 + - - +
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Residues in contact with GLN 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B IBM 2.8 39.0 + - - -
405B ASN* 6.1 1.0 - - - +
406B GLU* 2.8 37.3 + - - +
417B VAL* 3.8 30.0 - - + +
420B LEU* 4.6 4.5 - - - +
449B LYS 3.2 19.0 + - - +
452B ALA* 1.3 79.5 - - - +
454B ILE* 1.3 57.9 + - - +
455B GLY 3.5 0.2 - - - -
456B PHE* 4.2 8.1 - - - -
457B ILE* 2.8 40.7 + - + +
490B TYR* 3.9 22.2 - - + -
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Residues in contact with ILE 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B ALA 3.0 27.5 + - - +
451B THR* 4.1 5.4 + - - +
452B ALA 3.6 0.2 - - - -
453B GLN* 1.3 75.9 - - - +
455B GLY* 1.3 65.6 + - - +
457B ILE* 3.8 3.3 - - - +
458B LYS* 3.0 51.8 + - + +
459B PHE* 6.0 0.4 - - + -
487B ARG* 5.2 3.4 - - - +
490B TYR* 3.7 24.9 - - + +
491B GLU* 3.7 36.8 - - + +
494B LYS* 3.8 26.9 - - + -
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Residues in contact with GLY 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B THR 4.2 7.7 + - - -
452B ALA 5.0 0.2 - - - -
453B GLN 3.5 0.4 - - - -
454B ILE* 1.3 82.4 - - - +
456B PHE* 1.3 54.3 + - - +
459B PHE* 2.8 58.5 + - - +
460B VAL* 4.0 1.1 + - - +
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Residues in contact with PHE 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B IBM 3.3 81.9 - + + +
365B MET* 4.4 3.4 - - + -
403B ILE* 3.9 29.2 - - + -
406B GLU* 5.7 0.9 - - + -
452B ALA 3.6 19.8 + - - +
453B GLN* 3.3 14.9 + - - +
454B ILE 3.3 0.2 - - - -
455B GLY* 1.3 75.9 - - - +
457B ILE* 1.3 58.0 + - + +
460B VAL* 2.9 48.3 + - + +
461B LEU* 2.9 37.2 + - + -
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Residues in contact with ILE 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B GLU* 4.1 13.7 - - + -
453B GLN* 2.8 27.3 + - + +
454B ILE* 3.8 3.1 - - - +
456B PHE* 1.3 75.3 - - + +
458B LYS* 1.3 58.6 + - - +
461B LEU* 3.5 21.0 + - + -
462B ILE* 2.8 48.9 + - + +
483B LEU* 3.6 29.2 - - + +
486B SER* 3.3 31.0 - - - +
487B ARG* 3.9 14.6 - - + +
490B TYR* 4.0 15.3 - - + -
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Residues in contact with LYS 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B ILE* 3.0 34.8 + - + +
455B GLY 4.0 1.3 - - - +
457B ILE* 1.3 78.4 - - - +
459B PHE* 1.3 89.0 + - + +
462B ILE* 4.1 10.7 - - + +
463B PRO* 3.2 18.9 - - - +
487B ARG* 3.6 30.1 - - + +
491B GLU* 2.6 30.1 + - - +
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Residues in contact with PHE 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B HIS* 5.2 2.9 + - - -
454B ILE* 6.0 0.9 - - + -
455B GLY* 2.8 40.6 + - - +
458B LYS* 1.3 107.3 - - + +
460B VAL* 1.3 66.3 + - + +
463B PRO* 3.9 13.9 - - + +
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Residues in contact with VAL 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B IBM 4.6 8.7 - - + -
365B MET* 3.9 15.5 - - + -
368B HIS* 3.8 29.3 + - + +
403B ILE* 4.0 9.4 - - + -
455B GLY 4.9 0.4 - - - +
456B PHE* 2.9 48.9 + - + +
458B LYS 3.7 0.2 - - - -
459B PHE* 1.3 85.8 - - + +
461B LEU* 1.3 67.6 + - - +
462B ILE 3.7 0.4 - - - -
463B PRO* 3.6 1.8 - - - +
464B MET* 3.4 21.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il